Origin IGS: tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattttaagcctcaaagcaagtaaatccagttacgctgctttgcctgtactctccgtttcataaacgaaaaatgaacgggagtgttgtaaatatttttcgcaataatatcta Mask Tandem Repeat Region ================================================ tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Find is-nt database================================================ Query_seq: PI1308:PI1309|PI1308:PI1309:hypothetical protein:excinuclease ABC, A subunit:->->:1223778..1223890 113 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1308:PI1309|PI1308:PI1309:hypothetical protein:excinuclease ABC, A subunit:->->:1223778..1223890 113 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1308:PI1309|PI1308:PI1309:hypothetical protein:excinuclease ABC, A subunit:->->:1223778..1223890 113 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 6 End: 98 ..... M I A K N I Y N T P V H F S F M K R R V Q A K Q R N W I Y L L ............... tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1308:PI1309|PI1308:PI1309:hypothetical protein:excinuclease ABC, A subunit:->->:1223778..1223890 113 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: pint_PI1308_PI1309|hypothetical protein:excinuclease ABC, A subunit|POSITIVE:POSITIVE|[1223778,1223890]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta tagatattattgcgaaaaatatttacaacactcccgttcatttttcgtttatgaaacggagagtacaggcaaagcagcgtaactggatttacttgctttgaggcttaaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAUUAUUGCGAAAAAUAUUUACAACACUCCCGUUCAUUUUUCGUUUAUGAAACGGAGAGUACAGGCAAAGCAGCGUAACUGGAUUUACUUGCUUUGAGGCUUAAAAUUA ..(((.(((..((................((((((((((((.........))).))))).)))).....((((((((.((((......))))))))))))..)).))).))). (-24.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUAAGCCUCAAAGCAAGUAAAUCCAGUUACGCUGCUUUGCCUGUACUCUCCGUUUCAUAAACGAAAAAUGAACGGGAGUGUUGUAAAUAUUUUUCGCAAUAAUAUCUA .........((..(((((((.((((......))))..)))))))....(((((.(((((.(((.........)))))))))))))...............))........... (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 70 21 82 33 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 354 56 11 213 168 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 348 80 31 198 150 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 309 76 31 215 159 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 290 109 62 61 15 pint:PI1511|5end_hypothetical_protein_1429580..1429810_POSITIVE 288 79 35 174 137 pint:PI1403|5end_conserved_hypothetical_protein_1323920..1324150_POSITIVE 287 100 57 214 164 pint:PI1726|5end_ATP-dependent_DNA_helicase_1643402..1643632_POSITIVE 283 49 1 110 62 pint:PI0928|5end_hypothetical_protein_859851..860081_POSITIVE 283 104 68 204 159 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 282 50 2 136 89 pint:PI1905|5end_hypothetical_protein_1847628..1847858_POSITIVE 282 109 61 53 13 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 279 100 57 68 26 pint:PI2107|5end_hypothetical_protein_2059704..2059934_POSITIVE 278 96 51 143 91 pint:PI1893|5end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1835624..1835854_POSITIVE 275 80 31 75 21 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 272 96 56 75 30 pint:PI2029|5end_DNA_topoisomerase_I_1982775..1983005_POSITIVE 271 79 32 62 4 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 270 40 1 47 13 pint:PI1281|5end_hypothetical_protein_1196645..1196875_POSITIVE 270 86 46 140 86 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 270 86 46 66 12 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 266 100 55 184 143 pint:PI1299|5end_glycosyltransferase_1212191..1212421_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 70 21 149 100 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 303 76 35 104 62 pint:PI0060|3end_long-chain-fatty-acid--CoA_ligase_(acyl-CoA_synthetase)_60166..60316_POSITIVE 288 56 11 83 38 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 288 56 11 56 11 pint:PI2173|3end_hypothetical_protein_2113964..2114114_POSITIVE 284 86 46 87 46 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 271 79 32 62 4 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 270 86 46 140 86 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 268 95 51 102 55 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 265 74 34 57 14 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 262 80 39 54 10 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 258 79 31 54 4 pint:PI1902|3end_hypothetical_protein_1845175..1845325_POSITIVE 257 98 51 53 15 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 256 85 57 138 101 pint:PI0724|3end_DNA_polymerase_III,_delta_subunit_658601..658751_POSITIVE 256 75 31 88 42 pint:PI0545|3end_sugar_kinase_497867..498017_POSITIVE 255 103 69 108 77 pint:PI1474|3end_conserved_hypothetical_protein_1396969..1397119_POSITIVE 254 80 31 77 29 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 252 108 67 116 75 pint:PI0907|3end_NAD-dependent_DNA_ligase_836913..837063_POSITIVE 252 59 11 86 36 pint:PI0412|3end_primosomal_protein_N',_replication_factor_Y_382152..382302_POSITIVE 248 98 52 142 92 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 248 102 66 139 94 pint:PI1299|3end_glycosyltransferase_1213251..1213401_POSITIVE